User: florian.noack

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Posts by florian.noack

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Comment: C: question about DiffBind
... Hi Rory, I would like to use Diffbind to compare two Chip-seq data sets without replicates (replicates are in preparation but not finished yet). I tried your code but the dba.analyze function gives me following arrow message: Error in dimnames(x) <- dn :   length of 'dimnames' [1] not equal to a ...
written 9 months ago by florian.noack60
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Answer: A: Diffbind: edgeR or DESeq2 ?
... In other words you recommend not to use the substraction method but filter out peaks falling in the mention blacklist and set bSubControl=F ? About the csaw package: Iam not sure if a windowed approach is usefull in my case since I have quite "sharp" and seperated peaks (mostly around 125- 250 bp) ...
written 2.7 years ago by florian.noack60
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Answer: A: Diffbind: edgeR or DESeq2 ?
... Thanks a lot for the fast response from both of you. The samples I compare are linage related cell types and I know already from some other analysis which I did that I have only a few sites which show a different methylation  (3k out of 600k called peaks in the other approach I used) so I think edge ...
written 2.7 years ago by florian.noack60
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Diffbind: edgeR or DESeq2 ?
... Hi everybody, right now Iam trying to analyse my MeDip data set using Diffbind and Iam quite confused whather to use edgeR or DESeq2 for the analysis (iam a biologist with zero training in statistics and bioinformatics try to teach himself all the stuff). I tried already both options and DESeq2 giv ...
edger diffbind deseq2 medip-seq written 2.7 years ago by florian.noack60 • updated 13 months ago by Rory Stark2.6k

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Student 2.7 years ago, asked a question with at least 3 up-votes. For Diffbind: edgeR or DESeq2 ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Diffbind: edgeR or DESeq2 ?

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